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- PDB-3vp9: Crystal structure of the N-terminal domain of the yeast general c... -

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Basic information

Entry
Database: PDB / ID: 3vp9
TitleCrystal structure of the N-terminal domain of the yeast general corepressor Tup1p mutant
ComponentsGeneral transcriptional corepressor TUP1
KeywordsTRANSCRIPTION / Four helix bundle
Function / homology
Function and homology information


carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / mediator complex binding / hyperosmotic response / phosphatidylinositol-3,5-bisphosphate binding / transcription repressor complex / histone deacetylase binding / transcription corepressor activity / histone binding / negative regulation of DNA-templated transcription / DNA damage response ...carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / mediator complex binding / hyperosmotic response / phosphatidylinositol-3,5-bisphosphate binding / transcription repressor complex / histone deacetylase binding / transcription corepressor activity / histone binding / negative regulation of DNA-templated transcription / DNA damage response / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Transcriptional repressor Tup1, N-terminal / Tup N-terminal / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat ...Transcriptional repressor Tup1, N-terminal / Tup N-terminal / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / General transcriptional corepressor TUP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.799 Å
AuthorsMatsumura, H. / Kusaka, N. / Nakamura, T. / Tanaka, N. / Sagegami, K. / Uegaki, K. / Inoue, T. / Mukai, Y.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal structure of the N-terminal domain of the yeast general corepressor Tup1p and its functional implications
Authors: Matsumura, H. / Kusaka, N. / Nakamura, T. / Tanaka, N. / Sagegami, K. / Uegaki, K. / Inoue, T. / Mukai, Y.
History
DepositionFeb 28, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: General transcriptional corepressor TUP1
B: General transcriptional corepressor TUP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5256
Polymers22,1732
Non-polymers3524
Water3,135174
1
A: General transcriptional corepressor TUP1
B: General transcriptional corepressor TUP1
hetero molecules

A: General transcriptional corepressor TUP1
B: General transcriptional corepressor TUP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,05112
Polymers44,3464
Non-polymers7058
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area9400 Å2
ΔGint-45 kcal/mol
Surface area21340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.102, 41.461, 103.889
Angle α, β, γ (deg.)90.00, 95.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-227-

HOH

21A-231-

HOH

31A-247-

HOH

41B-259-

HOH

51B-263-

HOH

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Components

#1: Protein General transcriptional corepressor TUP1 / Flocculation suppressor protein / Glucose repression regulatory protein TUP1 / Repressor AER2


Mass: 11086.417 Da / Num. of mol.: 2 / Fragment: N-terminal domain / Mutation: L62R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: TUP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P16649
#2: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H8O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 14%(v/v) 1,4-dioxane, 0.1M MES monohydrate, 1.6M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.799→409 Å / Num. all: 20399 / Num. obs: 20399 / % possible obs: 91.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.8→1.83 Å / % possible all: 91.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.799→33.292 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8165 / SU ML: 0.14 / σ(F): 0 / Phase error: 25.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2575 941 4.84 %
Rwork0.2203 --
obs0.222 19436 87.02 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.794 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 98.04 Å2 / Biso mean: 45.7701 Å2 / Biso min: 14.38 Å2
Baniso -1Baniso -2Baniso -3
1--6.9989 Å2-0 Å29.9669 Å2
2---5.4813 Å2-0 Å2
3---12.4802 Å2
Refinement stepCycle: LAST / Resolution: 1.799→33.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1269 0 24 174 1467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071308
X-RAY DIFFRACTIONf_angle_d1.0711738
X-RAY DIFFRACTIONf_chiral_restr0.074177
X-RAY DIFFRACTIONf_plane_restr0.004230
X-RAY DIFFRACTIONf_dihedral_angle_d20.874518
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7993-1.89410.2731230.23772383250679
1.8941-2.01280.24611080.22552569267785
2.0128-2.16820.21051270.19972743287090
2.1682-2.38630.23721500.18742691284190
2.3863-2.73150.26981450.20792738288390
2.7315-3.44080.24251570.21332724288190
3.4408-33.29770.28371310.24232647277885

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